# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 00:28:55 2022
#   Inital geometry file: a 131 line input string
#   Ligand name: N~5~-{N-[2-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethoxy)ethyl]carbamimidoyl}-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)NCCOCCOCCOCCN=[N+]=N)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 56C  56C  N~5~-{N-[2-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethoxy)ethyl]carbamimidoyl}-L-ornithine  L-peptide  55  26  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_56C
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 56C  N    N  NH2    0  -0.785  -19.6003  16.9160  -19.2363
 56C  CA   C  CH1    0  -0.223  -19.2994  18.0586  -20.0860
 56C  C    C  C      0   0.389  -19.5922  19.4523  -19.4663
 56C  O    O  O      0  -0.617  -19.2932  20.4366  -20.1757
 56C  CB   C  CH2    0  -0.436  -20.0239  17.9115  -21.4270
 56C  CG   C  CH2    0  -0.450  -19.7671  16.6037  -22.1713
 56C  CD   C  CH2    0  -0.228  -18.2993  16.3811  -22.4988
 56C  NE   N  NH1    0  -0.666  -18.1355  15.1916  -23.3080
 56C  CZ   C  C      0   0.605  -16.8903  14.8241  -23.7381
 56C  NH1  N  N      0  -0.732  -15.8813  15.5925  -23.5268
 56C  C01  C  CH2    0  -0.142  -17.5808  11.7124  -25.6779
 56C  N01  N  NH1    0  -0.673  -16.8290  13.6483  -24.4525
 56C  O01  O  O2     0  -0.482  -18.6131  10.7679  -25.7538
 56C  C02  C  CH2    0  -0.332  -17.9086  12.6953  -24.5671
 56C  N02  N  N      0  -0.115  -16.7905   8.1812  -20.6749
 56C  O02  O  O2     0  -0.479  -19.7073   8.1664  -25.4706
 56C  C03  C  CH2    0  -0.175  -18.3900   9.7940  -26.7419
 56C  N03  N  N      1   0.533  -16.2023   8.4230  -19.7147
 56C  C04  C  CH2    0  -0.204  -19.5201   8.7849  -26.7192
 56C  N04  N  N      0  -0.335  -15.6781   8.5104  -18.6718
 56C  O04  O  O2     0  -0.469  -18.5158   8.2514  -22.9037
 56C  C05  C  CH2    0  -0.181  -18.7332   7.2174  -25.1170
 56C  C06  C  CH2    0  -0.216  -18.7324   7.0468  -23.6119
 56C  C07  C  CH2    0  -0.213  -17.2391   8.8073  -22.9839
 56C  C08  C  CH2    0  -0.366  -16.2486   8.1307  -22.0533
 56C  H1   H  HNH2   0   0.330  -19.1628  17.0627  -18.3348
 56C  H2   H  HNH2   0   0.320  -20.5943  16.9234  -19.0339
 56C  H4   H  HCH1   0   0.211  -18.2198  18.0375  -20.2832
 56C  OXT  O  OC    -1  -0.602  -20.0832  19.4825  -18.3209
 56C  H6   H  HCH2   0   0.218  -19.7452  18.7496  -22.0680
 56C  H7   H  HCH2   0   0.214  -21.1029  18.0046  -21.2571
 56C  H8   H  HCH2   0   0.216  -20.1425  15.7598  -21.5856
 56C  H9   H  HCH2   0   0.221  -20.3399  16.6145  -23.1035
 56C  H10  H  HCH2   0   0.217  -17.9110  17.2397  -23.0515
 56C  H11  H  HCH2   0   0.210  -17.7123  16.3155  -21.5762
 56C  H12  H  HNH1   0   0.392  -18.7766  14.4468  -23.0841
 56C  H13  H  H      0   0.310  -15.0547  15.2305  -23.9889
 56C  H14  H  HCH2   0   0.202  -16.6184  11.2210  -25.4671
 56C  H15  H  HCH2   0   0.211  -17.4634  12.2563  -26.6252
 56C  H16  H  HCH2   0   0.244  -18.8312  13.2189  -24.8253
 56C  H17  H  HCH2   0   0.206  -17.4176   9.3056  -26.5868
 56C  H18  H  HCH2   0   0.216  -18.3551  10.2406  -27.7461
 56C  H19  H  HCH2   0   0.235  -20.4605   9.2893  -26.9541
 56C  H20  H  HCH2   0   0.211  -19.3393   8.0532  -27.5180
 56C  H21  H  H      0   0.493  -15.5991   9.4620  -18.2915
 56C  H22  H  HCH2   0   0.212  -17.7344   7.5040  -25.4669
 56C  H23  H  HCH2   0   0.224  -18.9442   6.2382  -25.5693
 56C  H24  H  HCH2   0   0.245  -19.7059   6.6834  -23.2780
 56C  H25  H  HCH2   0   0.222  -17.9977   6.2742  -23.3539
 56C  H26  H  HCH2   0   0.277  -17.3247   9.8633  -22.7214
 56C  H27  H  HCH2   0   0.256  -16.7966   8.7658  -23.9857
 56C  H28  H  HCH2   0   0.338  -16.1376   7.0655  -22.2607
 56C  H29  H  HCH2   0   0.327  -15.2698   8.6086  -22.0776
 56C  H30  H  HNH1   0   0.382  -15.9047  13.2463  -24.4865
 56C  H3   H  HCH2   0   0.233  -18.0887  12.1437  -23.6347

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 56C  C03  C04  single  1.515  0.020  1.515
 56C  C03  O01  single  1.405  0.020  1.405
 56C  C05  C06  single  1.515  0.020  1.515
 56C  C05  O02  single  1.405  0.020  1.405
 56C  C07  C08  single  1.518  0.020  1.518
 56C  C07  O04  single  1.395  0.020  1.395
 56C  C04  O02  single  1.406  0.020  1.406
 56C  N    CA   single  1.458  0.019  1.458
 56C  O01  C01  single  1.401  0.020  1.401
 56C  C06  O04  single  1.414  0.020  1.414
 56C  C01  C02  single  1.519  0.020  1.519
 56C  C08  N02  single  1.482  0.020  1.482
 56C  N04  N03  double  1.171  0.020  1.171
 56C  N03  N02  double  1.152  0.020  1.152
 56C  C02  N01  single  1.445  0.020  1.445
 56C  CG   CB   single  1.526  0.020  1.526
 56C  CG   CD   single  1.520  0.020  1.520
 56C  NE   CZ   single  1.368  0.020  1.368
 56C  NE   CD   single  1.448  0.020  1.448
 56C  CB   CA   single  1.521  0.033  1.521
 56C  N01  CZ   single  1.377  0.020  1.377
 56C  CA   C    single  1.525  0.021  1.525
 56C  CZ   NH1  double  1.286  0.020  1.286
 56C  C    O    deloc   1.231  0.020  1.231
 56C  N    H1   single  0.890  0.020  1.040
 56C  N    H2   single  0.890  0.020  1.040
 56C  CA   H4   single  0.970  0.020  1.090
 56C  C    OXT  deloc   1.247  0.020  1.247
 56C  CB   H6   single  0.970  0.020  1.090
 56C  CB   H7   single  0.970  0.020  1.090
 56C  CG   H8   single  0.970  0.020  1.090
 56C  CG   H9   single  0.970  0.020  1.090
 56C  CD   H10  single  0.970  0.020  1.090
 56C  CD   H11  single  0.970  0.020  1.090
 56C  NE   H12  single  0.890  0.020  1.040
 56C  NH1  H13  single  0.890  0.020  1.040
 56C  C01  H14  single  0.970  0.020  1.090
 56C  C01  H15  single  0.970  0.020  1.090
 56C  C02  H16  single  0.970  0.020  1.090
 56C  C03  H17  single  0.970  0.020  1.090
 56C  C03  H18  single  0.970  0.020  1.090
 56C  C04  H19  single  0.970  0.020  1.090
 56C  C04  H20  single  0.970  0.020  1.090
 56C  N04  H21  single  0.890  0.020  1.040
 56C  C05  H22  single  0.970  0.020  1.090
 56C  C05  H23  single  0.970  0.020  1.090
 56C  C06  H24  single  0.970  0.020  1.090
 56C  C06  H25  single  0.970  0.020  1.090
 56C  C07  H26  single  0.970  0.020  1.090
 56C  C07  H27  single  0.970  0.020  1.090
 56C  C08  H28  single  0.970  0.020  1.090
 56C  C08  H29  single  0.970  0.020  1.090
 56C  N01  H30  single  0.890  0.020  1.040
 56C  C02  H3   single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 56C  H2   N    H1   104.16  3.000
 56C  H2   N    CA   108.26  3.000
 56C  H1   N    CA   108.46  3.000
 56C  H4   CA   CB   107.83  3.000
 56C  H4   CA   C    105.93  3.000
 56C  CB   CA   C    110.50  1.500
 56C  H4   CA   N    107.05  3.000
 56C  C    CA   N    111.00  2.800
 56C  CB   CA   N    110.40  1.500
 56C  OXT  C    O    126.64  3.000
 56C  OXT  C    CA   120.80  1.700
 56C  O    C    CA   120.80  1.700
 56C  H7   CB   H6   106.09  3.000
 56C  H7   CB   CG   108.30  3.000
 56C  H6   CB   CG   109.19  3.000
 56C  H7   CB   CA   108.77  3.000
 56C  H6   CB   CA   108.64  3.000
 56C  CG   CB   CA   115.45  3.000
 56C  H9   CG   H8   106.51  3.000
 56C  H9   CG   CD   108.86  3.000
 56C  H8   CG   CD   109.50  3.000
 56C  H9   CG   CB   108.60  3.000
 56C  H8   CG   CB   110.01  3.000
 56C  CD   CG   CB   113.13  3.000
 56C  H11  CD   H10  106.42  3.000
 56C  H11  CD   NE   111.15  3.000
 56C  H10  CD   NE   108.83  3.000
 56C  H11  CD   CG   110.16  3.000
 56C  H10  CD   CG   109.69  3.000
 56C  NE   CD   CG   110.48  3.000
 56C  H12  NE   CZ   116.77  3.000
 56C  H12  NE   CD   114.26  3.000
 56C  CZ   NE   CD   119.96  3.000
 56C  N01  CZ   NH1  124.09  3.000
 56C  NH1  CZ   NE   120.15  3.000
 56C  N01  CZ   NE   115.66  3.000
 56C  H13  NH1  CZ   110.58  3.000
 56C  H15  C01  H14  107.02  3.000
 56C  H15  C01  C02  109.46  3.000
 56C  H14  C01  C02  109.72  3.000
 56C  H15  C01  O01  111.45  3.000
 56C  H14  C01  O01  110.71  3.000
 56C  C02  C01  O01  108.47  3.000
 56C  H30  N01  C02  114.79  3.000
 56C  H30  N01  CZ   113.49  3.000
 56C  C02  N01  CZ   124.82  3.000
 56C  C03  O01  C01  112.85  3.000
 56C  H3   C02  H16  107.65  3.000
 56C  H3   C02  N01  112.74  3.000
 56C  H16  C02  N01  109.51  3.000
 56C  H3   C02  C01  109.34  3.000
 56C  H16  C02  C01  108.65  3.000
 56C  N01  C02  C01  108.88  3.000
 56C  C08  N02  N03  126.57  3.000
 56C  C05  O02  C04  115.36  3.000
 56C  H18  C03  H17  106.33  3.000
 56C  H18  C03  C04  107.93  3.000
 56C  H17  C03  C04  111.21  3.000
 56C  H18  C03  O01  111.45  3.000
 56C  H17  C03  O01  110.44  3.000
 56C  C04  C03  O01  109.43  3.000
 56C  N04  N03  N02  170.83  3.000
 56C  H20  C04  H19  107.03  3.000
 56C  H20  C04  C03  108.06  3.000
 56C  H19  C04  C03  109.34  3.000
 56C  H20  C04  O02  112.02  3.000
 56C  H19  C04  O02  106.23  3.000
 56C  C03  C04  O02  113.93  3.000
 56C  H21  N04  N03  115.67  3.000
 56C  C07  O04  C06  116.80  3.000
 56C  H23  C05  H22  106.05  3.000
 56C  H23  C05  C06  107.98  3.000
 56C  H22  C05  C06  110.25  3.000
 56C  H23  C05  O02  111.41  3.000
 56C  H22  C05  O02  112.00  3.000
 56C  C06  C05  O02  109.05  3.000
 56C  H25  C06  H24  106.91  3.000
 56C  H25  C06  C05  108.27  3.000
 56C  H24  C06  C05  109.94  3.000
 56C  H25  C06  O04  112.31  3.000
 56C  H24  C06  O04  105.49  3.000
 56C  C05  C06  O04  113.69  3.000
 56C  H27  C07  H26  106.74  3.000
 56C  H27  C07  C08  106.26  3.000
 56C  H26  C07  C08  109.57  3.000
 56C  H27  C07  O04  114.02  3.000
 56C  H26  C07  O04  107.46  3.000
 56C  C08  C07  O04  112.61  3.000
 56C  H29  C08  H28  109.43  3.000
 56C  H29  C08  C07  112.15  3.000
 56C  H28  C08  C07  112.64  3.000
 56C  H29  C08  N02  109.53  3.000
 56C  H28  C08  N02  104.31  3.000
 56C  C07  C08  N02  108.44  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 56C  CONST_01  N01  CZ   NE   CD    180.00   0.0  0
 56C  CONST_02  NH1  CZ   NE   CD      0.00   0.0  0
 56C  CONST_03  C02  N01  CZ   NE      0.00   0.0  0
 56C  CONST_04  C02  N01  CZ   NH1   180.00   0.0  0
 56C  CONST_06  H13  NH1  CZ   NE    180.00   0.0  0
 56C  Var_01    CD   CG   CB   CA    -59.38  30.0  1
 56C  Var_02    NE   CD   CG   CB   -174.76  30.0  3
 56C  Var_03    CZ   NE   CD   CG    178.65  30.0  1
 56C  Var_04    C01  C02  N01  CZ    166.93  30.0  2
 56C  Var_05    C04  C03  O01  C01   177.72  30.0  1
 56C  Var_06    O01  C01  C02  N01   178.19  30.0  2
 56C  Var_07    O02  C04  C03  O01   -56.51  30.0  3
 56C  Var_08    O04  C07  C08  N02   -55.48  30.0  1
 56C  Var_09    O04  C06  C05  O02   -56.78  30.0  3
 56C  Var_10    C07  C08  N02  N03  -137.55  30.0  1
 56C  Var_11    C06  C05  O02  C04   158.04  30.0  1
 56C  Var_12    C08  C07  O04  C06   -79.79  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 56C  chir_01  CA  N  CB  C  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 56C  plan-1  CD   0.020
 56C  plan-1  NE   0.020
 56C  plan-1  CZ   0.020
 56C  plan-1  NH1  0.020
 56C  plan-1  N01  0.020
 56C  plan-1  C02  0.020
 56C  plan-1  H12  0.020
 56C  plan-1  H13  0.020
 56C  plan-1  H30  0.020
 56C  plan-2  CA   0.020
 56C  plan-2  C    0.020
 56C  plan-2  O    0.020
 56C  plan-2  OXT  0.020
 56C  plan-3  N02  0.020
 56C  plan-3  N03  0.020
 56C  plan-3  N04  0.020
 56C  plan-3  C08  0.020
 56C  plan-3  H21  0.020

